Well, after a week of doubt, delays and fears of a military coup, last Sunday to the cheers and jubilation of a massive crowd in Cairo's Tahrir Square, Dr. Mohammed Morsi was declared winner in the presidential election. According to the Election Commission, nearly 52% of the votes were cast in his favor; his opponent General Ahmed Shafiq - an old guard from the Hosni Mubarak era - received nearly 48% of the votes.

So, for the first time in modern Egypt, her people had chosen one of their own in a free election. I am glad to note that Dr. Morsi is a fellow alumnus from my school – the University of Southern California, Los Angeles, where he earned his PhD in engineering.

With the official announcement, one would suppose that everything is going in the right direction and there is nothing to feel concerned about the emerging democracy in Egypt – the land which had seen more Pharaohs than democratically elected rulers. However, serious challenges remain, as the ruling military council has effectively stripped the incoming president of most of his powers. Morsi's recognition as president, thus, does little to resolve the larger standoff between the generals and the Brotherhood over the institutions of government and the future constitution.

The real power in Egypt is still with the Supreme Council of Armed Forces (SCAF), which has been running the country for the past 16 months after the revolution forced Hosni Mubarak to step down! It is a military junta comprising of “19 Mubaraks” - who were all hand-picked by the last dictator to protect his regime. Thus, while Mubarak is gone and enjoying the comfort of military hospital instead of jail, his partners-in-crime and beneficiaries have still been holding their power behind that all-powerful clique. There is widespread perception that this unelected few are determined to retain as much power necessary to dominate Egyptian politics and preserve their perks.

Thus, we are not too surprised to learn that the Supreme Council has over the past week given itself the role of legislator, the right to arrest civilians, control over drafting a new constitution and stripped the next president of many significant powers. It has dissolved the popularly elected Parliament, dominated by the Muslim Brotherhood, and has passed decrees to shield the military from civilian oversight so that none can contest its overwhelming power, and not even the newly elected president. Such moves have been called the silent coup.

The military has already been blamed by critics for mismanaging the 16-month transition since Mubarak's overthrow and a host of gross rights abuses, including the killing of protesters, torturing detainees and hauling more than 12,000 civilians for trial before military tribunals since it took power.

These moves have been condemned by the Human Rights Watch which said last Thursday that recent moves by Egypt's ruling generals suggested that there would not be a "meaningful" handover of power to civilian rule by July 1 as promised. In a statement, the New York-based group said the generals created conditions that are "ripe" for further abuses. "The generals' relentless expansion of their authority to detain and try civilians now goes far beyond their powers under Hosni Mubarak," the statement quoted the group's Middle East director, Joe Stork, as saying.

The true intention of the SCAF remains unclear. As recently as Sunday morning, Cairo was tense with fears that the panel of Mubarak-appointed judges overseeing the vote would declare Shafiq president. Banks, schools and government offices closed early for fear of violence in the streets. Tens of thousands of Brotherhood supporters and allies against military rule had gathered in Cairo's Tahrir Square for the sixth day of a sit-in demanding the military roll back its power grab. Then came the moment when it was announced that Dr. Morsi had won the run-off election.

Even with that announcement the Egyptian crisis is still far from over. Will SCAF grant Dr. Morsi the power necessary to govern effectively or set him up to fail so that it could torpedo the revolution? Will Dr. Morsi be able to curb the power of the military junta? Will he be able to influence the drafting of a new constitution that respects civil rights and represents the aspirations of his people? Will he be a unifying leader?

In his first nationally televised speech on Sunday, Dr. Morsi vowed to represent all Egyptians and urged his countrymen to put aside their differences and come together for the common good. He said, "This national unity is the only way to get Egypt out of this difficult crisis." He also paid special tribute to those 900 "martyrs" who helped spearhead the revolution that led to the ouster of Egypt's longtime President Hosni Mubarak and, more than a year later, to his own election win.

Dr. Morsi is a pragmatist. Fulfilling a campaign pledge to represents all Egyptians, he has resigned from the Brotherhood, and its political arm – the Freedom and Justice Party. But for Dr. Morsi to succeed, he will need a legislative ally. He had that ally in the now-dissolved parliament. Although the SCAF has said elections will be held for a new legislature, the revolutionaries mistrust such promises, and see its dirty-hand in dissolving the parliament. They say they will continue their sit-ins at Tahrir Square and fight in the courts until the disbanded parliament is restored.

Recently, an Egyptian court has suspended a government decision allowing military police and intelligence to arrest civilians. This is a small but important victory for the people of Egypt who are not afraid any more to demand what is fair. They are fighting back through the legal channels and peaceful protests to contest military decrees that are unfair. Neither bayonet nor bullet is going to take away their hard-earned victory.

Egypt is the Arab world’s most populous country. With millions of educated but unemployed young people, a corrupt oligarchy that controls private industry, and a massive underclass, the Egyptian people care more about economy and employment than anything else. And at the end, that is how Dr. Morsi will be judged by his people.

So, the serious questions remain as to with all the major powers stripped, and the parliament dissolved, how effective would Dr. Morsi be to bring food to the table of those hungry millions? Will he be able to nudge the army to restore presidential powers it curtailed this month through negotiation and pressure so that he could fulfill the dreams of the revolutionaries and those martyrs? Only the coming months would show if revolution has been issued a death certificate or a healthy bill of life.